I'm not sure Nintendo is pleased with the franchise. I think there was the hope to bring Metal Gear to Nintendo consoles in a bigger way and it DID happen at first. But then I guess they didn't preform well enough and Metal Gear has for a while now basically not been on Nintendo things and chosen other consoles. People might underestimate how much that might tick off Nintendo. Back when Brawl came out Metal Gear appeared to be going Nintendo pretty strongly with remakes and stuff. But that's over. Even if Sakurai and that other d00d are friends I'm not sure that's enough. Nintendo might just not want it to happen since they're not getting anything out of the deal anymore since Metal Gear isn't going with Nintendo anymore.
On the other hand Mega Man is constantly with Nintendo in some form. Same with Sonic.
Then again he could be back, I'm not psychic. I think his chances are not strong though. Snake in this game would mainly serve as a Metal Gear advertisement for Metal Gear games that currently go pretty exclusively to Nintendo's competition.
Who's not to say there won't be a Metal Gear for the Wii U? Now, let's recap every Metal Gear game on a Nintendo console:
Metal Gear (NES) (Hated by Kojima, didn't work on it)
Snake's Revenge (NES) (The non-canon sequel to Metal Gear for the NES)
Metal Gear: Ghost Babel (GBC) (Critically acclaimed, considered one of the best Gameboy Color games ever)
Metal Gear Solid: The Twin Snakes (GC) (A remake of Metal Gear Solid, once again, highly praised for updating everything)
Metal Gear Solid: Snake Eater 3D (3DS) (A remake of Snake Eater, which was developed from scratch and, although everyone wasn't a big fan of the choppiness of the 3DS and strange controls, loved it)
Now, that leaves us with 5 Metal Gear games. And like I said, there could be more on their way. And, let's be honest, I'd be worried about my game selling on Wii U as well, due to its poor sales recently. I think that's why Kojima's so hesitant. Do you kinda see the situation now? Perhaps it's likely or unlikely from a personal type of view, but in a general view, it's a 50/50, no matter what (at least, for now). In a way, it's like the Ridley situation. We haven't seen full evidence supporting them coming back/being playable, but neither have we seen them 100% deconfirmed.